(Q38844572)

19 October 2017

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics (English)

1 reference

Felipe da Veiga Leprevost

19 October 2017

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Dmitry Avtonomov

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Dattatreya Mellacheruvu

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Alexey I. Nesvizhskii

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

author name string

Andy T Kong

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

publication date

10 April 2017

1 reference

19 October 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

volume

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

page(s)

513-520

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1038/nmeth.4256

5 June 2020

exact match

0 references

cites work

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17 June 2018

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Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides

17 June 2018

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Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search

17 June 2018

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The BioPlex Network: A Systematic Exploration of the Human Interactome

17 June 2018

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A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

17 June 2018

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pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data

17 June 2018

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The proteomic landscape of triple-negative breast cancer

17 June 2018

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DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

17 June 2018

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Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing.

17 June 2018

1 reference

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Proteogenomics: concepts, applications and computational strategies

17 June 2018

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Crux: rapid open source protein tandem mass spectrometry analysis

17 June 2018

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Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins.

17 June 2018

1 reference

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Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling

17 June 2018

1 reference

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Making proteomics data accessible and reusable: current state of proteomics databases and repositories

17 June 2018

1 reference

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DeMix workflow for efficient identification of cofragmented peptides in high resolution data-dependent tandem mass spectrometry

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS

17 June 2018

1 reference

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Hunting for unexpected post-translational modifications by spectral library searching with tier-wise scoring

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD).

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Transferred subgroup false discovery rate for rare post-translational modifications detected by mass spectrometry

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Enzymology of H2S biogenesis, decay and signaling

17 June 2018

1 reference

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Comet: an open-source MS/MS sequence database search tool

17 June 2018

1 reference

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Fast multi-blind modification search through tandem mass spectrometry

17 June 2018

1 reference

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Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

17 June 2018

1 reference

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A face in the crowd: recognizing peptides through database search

17 June 2018

1 reference

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Faster SEQUEST searching for peptide identification from tandem mass spectra

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

QuickMod: A tool for open modification spectrum library searches

17 June 2018

1 reference

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Andromeda: a peptide search engine integrated into the MaxQuant environment

17 June 2018

1 reference

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Sequence tagging reveals unexpected modifications in toxicoproteomics

17 June 2018

1 reference

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SAINT: probabilistic scoring of affinity purification-mass spectrometry data

17 June 2018

1 reference

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A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

17 June 2018

1 reference

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Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies.

17 June 2018

1 reference

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Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets

17 June 2018

1 reference

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A guided tour of the Trans-Proteomic Pipeline

17 June 2018

1 reference

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PTMap--a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites.

17 June 2018

1 reference

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Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Protein identification by spectral networks analysis

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

TANDEM: matching proteins with tandem mass spectra

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

A statistical model for identifying proteins by tandem mass spectrometry

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Error tolerant searching of uninterpreted tandem mass spectrometry data

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Quantifying protein measurands by peptide measurements: where do errors arise?

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Deconvolution of mixture spectra and increased throughput of peptide identification by utilization of intensified complementary ions formed in tandem mass spectrometry.

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Unrestrictive identification of post-translational modifications through peptide mass spectrometry

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures.

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Identification of formaldehyde-induced modifications in proteins: reactions with model peptides

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5409104

Illuminating the dark matter of shotgun proteomics

22 August 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.4256

7 January 2021

Extent of Modifications in Human Proteome Samples and Their Effect on Dynamic Range of Analysis in Shotgun Proteomics

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.4256

7 January 2021

Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.4256

7 January 2021

System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.4256

7 January 2021

Construction of protein interaction networks based on the label-free quantitative proteomics

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.4256

7 January 2021

Comprehensive analysis of mouse retinal mononuclear phagocytes.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.4256

7 January 2021

Identifiers

DOI

10.1038/NMETH.4256

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

5 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28394336%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

PubMed publication ID

28394336

1 reference